Glycine residues

Biosynthesis. Two closely related genes encode the three mammalian tachykinins. The preprotachykinin A gene encodes both substance P and substance K, while the preprotachykinin B gene encodes neuromedin K (45—47). The active sequences are flanked by the usual double-basic amino acid residues, and the carboxy-terrninal amino acid is a glycine residue which is decarboxylated to an amide. As with most neuropeptide precursors, intermediates in peptide processing can be detected, but their biological activities are not clear (ca 1994). 

Glycine residues can adopt many different conformations... 

How would substrate preference be changed if the glycine residues in trypsin at positions 216 and 226 were changed to alanine rather than to the more bulky valine and threonine groups that are present in elastase This question was addressed by the groups of Charles Cralk, William Rutter, and Robert Fletterick in San Francisco, who have made and studied three such trypsin mutants one in which Ala is substituted for Gly at 216, one in which the same substitution is made at Gly 226, and a third containing both substitutions. 

Glycine residues have more conformational freedom than any other amino acid, as discussed in Chapter 1. A glycine residue at a specific position in a protein has usually only one conformation in a folded structure but can have many different conformations in different unfolded structures of the same protein and thereby contribute to the diversity of unfolded conformations. Proline residues, on the other hand, have less conformational freedom in unfolded structures than any other residue since the proline side chain is fixed by an extra covalent bond to the main chain. Another way to decrease the number of possible unfolded structures of a protein, and hence stabilize the native structure, is, therefore, to mutate glycine residues to any other residue and to increase the number of proline residues. Such mutations can only be made at positions that neither change the conformation of the main chain in the folded structure nor introduce unfavorable, or cause the loss of favorable, contacts with neighboring side chains. 

Myristic acid may be linked via an amide bond to the a-amino group of the N-terminal glycine residue of selected proteins (Figure 9.18). The reaction is referred to as A -myristoylation and is catalyzed by myristoyl—CoAtprolein N-myris-toyltransferase, known simply as NMT. A -Myristoyl-anchored proteins include the catalytic subunit of cAMP-dependent protein kinase, the ppSff tyrosine kinase, the phosphatase known as calcineurin B, the a-subunit of G proteins (involved in GTP-dependent transmembrane signaling events), and the gag proteins of certain retroviruses, including the FHV-l virus that causes AIDS. 

It has been shown that glyeine amides of aminobenzophenones are readily converted to the corresponding benzodiazepines in vivo. Peptides which terminate in such a moiety should thus serve as a benzodiazepine prodrug after hydrolysis by peptidases. One of the glycine residues in lorzafone (194)is presumably removed metabolicaUy in this manner to give a benzodiazepine precursor which spontaneously cyclizes. Acylation of benzophenone 190 with the trityl protected dipeptide 191, as its acid chloride 192, affords the amide 193. Removal of the trityl protecting group with acid yields lorzafone (194) [50]. 

Only a few residues show more than 75% sequence identity, including four glycine residues, a proline residue at the beginning of the Pro loop, and a phenylalanine residue in a position corresponding to the conserved residue Tyr 165 of the bovine heart Rieske protein. However, structure prediction and sequence comparison with Rieske proteins from bci complexes suggests that the fold will be very similar in all Rieske-type ferredoxins, as in the other Rieske or Rieske-type proteins (see Section III,B,1). 

Peptoids based on a-chiral aliphatic side chains can form stable helices as well [43]. A crystal of a pentameric peptoid homooligomer composed of homochiral N-(1-cyclohexylethyl)glycine residues was grown by slow evaporation from methanol solution, and its structure determined by X-ray crystallographic methods. In the crystalline state, this pentamer adopts a helical conformation with repeating cis-... 

The receptors range in size from 379 to 595 amino acids. The receptors have two transmembrane regions with intracellular N- and C-termini (Figure 3.11). Extensive SCAM analysis suggests that TM2 forms the pore, and a conserved glycine residue in the middle of TM2 lines the narrowest part of the channel. The structure of the pore and the location of the gate have still not been... 

Amino acids are characteristic examples of compounds with an asymmetric carbon atom, with the exception of glycine which, since its a-carbon carries two hydrogens, is often said to be without an asymmetric carbon atom. As a typical C(abc2) system, glycine can be used (Schafer et al. 1984G) to illustrate the conformationally dependent chirality of tetrahedral carbon atoms with two substituents of identical constitution. That is, in compounds containing the glycine residue, some conformations usually exist in which the a-carbon is asymmetric and others in which it is not. 

For simple calculations such as the one given above, a linear parametrization of the Hamiltonian is sufficient. However in most cases, one is interested in growing new atoms or removing atoms. This is the case if for example one is transforming a glycine residue into an alanine. See Fig. 4.14. 

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